Font size: Increase font size Decrease font size Switch style sheet from default to highcontrast and back



barriers − manual page for barriers 1.8.1


barriers [OPTION]... [[FILE]]...


barriers 1.8.1

Compute local minima and energy barriers of a landscape

This program reads an energy sorted list of conformations of a landscape, and computes local minima and energy barriers of the landscape. For RNA secondary structures, suitable input is produced by RNAsubopt. For each local minimum found it prints to stdout, the conformation of the minimum, its energy, the number of the "parent"−minimum it merges with, and the height of the energy barrier. Additional information on each minimum, such as saddle point conformation and basin sizes can be included via options.

A PostScript drawing of the resulting tree is written to "" in the current directory.
, −−help

Print help and exit


Print help, including all details and hidden options, and exit


Print help, including hidden options, and exit

−V, −−version

Print version and exit

General Options:

Command line options which alter the general behavior of this program.

−v, −−verbose

Be verbose, i.e. print more information. (default=off)

−q, −−quiet

Be quiet (also inhibit PS tree output). (default=off)

Graphs and Move Sets:

The graph and move set options specify the types of states/conformations in the system as well as their neighborhood. Some graphs provide different neighborhood settings. The type of landscape may also be set by the input file using the fourth word on first line. E.g.:


for a landscape of canonical RNA structures.

−G, −−graph=Graph

Define type of the graph, i.e. configuration space. (default=‘RNA’)

The configuration space (graph) determines the neighborhood of the system and can be any of the following types:

’RNA’: RNA secondary structures

’RNA−noLP’: canonical RNA structures

’RNA2’: RNA secondary structures

’RNA2−noLP’: canonical RNA structures, no lonely pairs

’Q2’: Spin Glass (strings of "+−")

’Qa,ALPHA’: a−letter Hamming graph, e.g. Q3 strings of "ABC". ALPHAbet is

optional, default is ’ABC...’

’T’: Phylogenetic Treesin bracket notation, e.g. "((1)(((2)(3))(5))(4))"

’P’: Permutations as comma separated list, e.g. 5,1,4,2,3

’X’: Exchange Moves on balances +/− strings

’?’: General graph; adjacency list in file

−M, −−moves=STRING

Select the move−set for generating neighbors of a configuration (if Graph allows several different ones).

The available move sets heavily depend on the choice of the graph. For RNA structures, the available move sets are:

’[no]Shift’: (Dis−)allow shift moves. (default: noShift)

’ligand’: RNA−ligand/protein interaction

For permutation graphs, the possible move sets are:

’T’: for Transpositions (default)

’C’: for Canonical Transpositions

’R’: for Reversal moves.

Spin Glass graphs provide the two move sets:

’p’: point mutations, i.e. single spin flip (default), and

’c’: flip 2nd half.

Trees always use NNI (Nearest Neighbour Interchange).


Input is a poset from n objective functions. (default=‘0’)

Barrier Tree Computation:
, −−connected

Restrict the output to the connected component. (default=off)

Depending on the input data, the corresponding barrier tree(s) might not be connected, i.e. the internal representation actually is a barrier forest. Enabling this option will restrict the output to the one connected component the ground state belongs to. In case there are multiple ground states that belong to different trees, the first (according to the input order) will be selected. Note, that restricting the rate computation to the connected component also ensures that the rate matrix is ergodic.


Print the size of of each basin in output. (default=off)


Print saddle component sizes. (default=off)


Compute only the lowest <num> local minima. (default=‘100’)


Print only minima with energy barrier greater than delta. (default=‘0.000001’)


Print the saddle point conformations in output. (default=off)

Transition Rate Computation:

Compute rates between macro states (basins). (default=off)

Two output files are written, "rates.out" containing the rates in ASCII format and "rates.bin" in binary form. Both output files can be readily used in conjunction with the treekin program.


Specify file name for the rates output.



Specify file name for the binary rates output.



Scale rates of double moves for RNA−noLP (e.g. 0.01). (default=‘1.0’)


Compute microscopic rates between connected states. (default=off)

−T, −−temp=DOUBLE

Set temperature in degree centigrade. (default=‘37.0’)

This temperature is used to compute Boltzmann fators in conjunction with −−rates option.

Miscellaneous Options:
, −−path=<l1>=<l2>

Backtrack an optimal path between local minimum l2 and l1.

The option can be specified multiple times and each path will be written to a corresponding file "path.l1.l2.txt".


Map conformations to minima in the tree.

Once the barrier tree (and optionally rates) are constructed , read stuctures from "filename" and map them to their corresponding minima (macro states). Output is written to file "mapstruc.out" in table format with the following columns:

1: gradient_min

2: index_in_subopt

3: energy

4: basin

5: truebasin

6: gradient_basin

7: true_grad_basin

The last number is probably what you want, true basins are those that fulfill the minh criterium.


Specify the filename for structure mapping output. (default=‘mapstruc.out’)


Ch. Flamm, I.L. Hofacker, P.F. Stadler, M.T. Wolfinger. "Barrier trees of degenerate landscapes" Z. Phys. Chem., 216:155−173 (2002)

Ligand support has been added with version 1.7.0, see

M.T. Wolfinger, Ch. Flamm, I.L. Hofacker "Efficient computation of cotranscriptional RNA-ligand interaction dynamics" Methods, (2018)


Ivo Hofacker, Christoph Flamm, Peter Stadler, Michael T. Wolfinger